Problem while updating

PiUser · 11. Mai 2023

Hello,

I just tried to update my OMV and got folling error message in the Web GUI:

Zitat

Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
Python path configuration: PYTHONHOME = (not set) PYTHONPATH = (not set) program name = '/usr/bin/python3' isolated = 0 environment = 1 user site = 1 import site = 1 sys._base_executable = '/usr/bin/python3' sys.base_prefix = '/usr' sys.base_exec_prefix = '/usr' sys.platlibdir = 'lib' sys.executable = '/usr/bin/python3' sys.prefix = '/usr' sys.exec_prefix = '/usr' sys.path = [ '/usr/lib/python39.zip', '/usr/lib/python3.9', '/usr/lib/python3.9/lib-dynload', ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
ValueError: source code string cannot contain null bytes

Current thread 0x76f5d980 (most recent call first):
<no Python frame>
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Setting up openmediavault (6.3.10-2) ...
Creating configuration database ...
Python path configuration: PYTHONHOME = (not set) PYTHONPATH = (not set) program name = 'python3' isolated = 0 environment = 1 user site = 1 import site = 1 sys._base_executable = '/usr/bin/python3' sys.base_prefix = '/usr' sys.base_exec_prefix = '/usr' sys.platlibdir = 'lib' sys.executable = '/usr/bin/python3' sys.prefix = '/usr' sys.exec_prefix = '/usr' sys.path = [ '/usr/lib/python39.zip', '/usr/lib/python3.9', '/usr/lib/python3.9/lib-dynload', ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
ValueError: source code string cannot contain null bytes

Current thread 0x76fd2980 (most recent call first):
<no Python frame>
dpkg: error processing package openmediavault (--configure): installed openmediavault package post-installation script subprocess returned error exit status 1
Errors were encountered while processing: openmediavault
** CONNECTION LOST **
█

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The same error occurs when I tried to run apt update via ssh.

Any thoughts?

Michael

Soma · 11. Mai 2023

Zitat von PiUser

The same error occurs when I tried to run apt update via ssh.

Post the output inside a codebox of:

sudo omv-upgrade

PiUser · 11. Mai 2023

it is more or less the same error:

Code

pi@omv:~ $ sudo omv-upgrade
Get:1 file:/var/cache/openmediavault/archives  InRelease
Ign:1 file:/var/cache/openmediavault/archives  InRelease
Get:2 file:/var/cache/openmediavault/archives  Release
Ign:2 file:/var/cache/openmediavault/archives  Release
Get:3 file:/var/cache/openmediavault/archives  Packages
Ign:3 file:/var/cache/openmediavault/archives  Packages
Get:4 file:/var/cache/openmediavault/archives  Translation-en
Ign:4 file:/var/cache/openmediavault/archives  Translation-en
Get:3 file:/var/cache/openmediavault/archives  Packages
Ign:3 file:/var/cache/openmediavault/archives  Packages
Get:4 file:/var/cache/openmediavault/archives  Translation-en
Ign:4 file:/var/cache/openmediavault/archives  Translation-en
Get:3 file:/var/cache/openmediavault/archives  Packages
Ign:3 file:/var/cache/openmediavault/archives  Packages
Get:4 file:/var/cache/openmediavault/archives  Translation-en
Ign:4 file:/var/cache/openmediavault/archives  Translation-en
Get:3 file:/var/cache/openmediavault/archives  Packages
Ign:3 file:/var/cache/openmediavault/archives  Packages
Get:4 file:/var/cache/openmediavault/archives  Translation-en
Ign:4 file:/var/cache/openmediavault/archives  Translation-en
Get:3 file:/var/cache/openmediavault/archives  Packages
Ign:3 file:/var/cache/openmediavault/archives  Packages
Get:4 file:/var/cache/openmediavault/archives  Translation-en
Ign:4 file:/var/cache/openmediavault/archives  Translation-en
Get:3 file:/var/cache/openmediavault/archives  Packages
Ign:3 file:/var/cache/openmediavault/archives  Packages
Get:4 file:/var/cache/openmediavault/archives  Translation-en
Ign:4 file:/var/cache/openmediavault/archives  Translation-en
Get:3 file:/var/cache/openmediavault/archives  Packages
Get:4 file:/var/cache/openmediavault/archives  Translation-en
Ign:4 file:/var/cache/openmediavault/archives  Translation-en
Hit:5 http://packages.openmediavault.org/public shaitan InRelease
Get:6 http://raspbian.raspberrypi.org/raspbian bullseye InRelease [15.0 kB]
Hit:7 http://archive.raspberrypi.org/debian bullseye InRelease
Hit:8 https://openmediavault.github.io/packages shaitan InRelease
Fetched 15.0 kB in 2s (6827 B/s)
Python path configuration:
  PYTHONHOME = (not set)
  PYTHONPATH = (not set)
  program name = 'python3'
  isolated = 0
  environment = 1
  user site = 1
  import site = 1
  sys._base_executable = '/usr/bin/python3'
  sys.base_prefix = '/usr'
  sys.base_exec_prefix = '/usr'
  sys.platlibdir = 'lib'
  sys.executable = '/usr/bin/python3'
  sys.prefix = '/usr'
  sys.exec_prefix = '/usr'
  sys.path = [
    '/usr/lib/python39.zip',
    '/usr/lib/python3.9',
    '/usr/lib/python3.9/lib-dynload',
  ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
ValueError: source code string cannot contain null bytes

Current thread 0x76fd2980 (most recent call first):
<no Python frame>
Reading package lists... Done
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Calculating upgrade... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Python path configuration:
  PYTHONHOME = (not set)
  PYTHONPATH = (not set)
  program name = '/usr/bin/python3'
  isolated = 0
  environment = 1
  user site = 1
  import site = 1
  sys._base_executable = '/usr/bin/python3'
  sys.base_prefix = '/usr'
  sys.base_exec_prefix = '/usr'
  sys.platlibdir = 'lib'
  sys.executable = '/usr/bin/python3'
  sys.prefix = '/usr'
  sys.exec_prefix = '/usr'
  sys.path = [
    '/usr/lib/python39.zip',
    '/usr/lib/python3.9',
    '/usr/lib/python3.9/lib-dynload',
  ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
ValueError: source code string cannot contain null bytes

Current thread 0x76f1f980 (most recent call first):
<no Python frame>
Setting up openmediavault (6.3.10-2) ...
Creating configuration database ...
Python path configuration:
  PYTHONHOME = (not set)
  PYTHONPATH = (not set)
  program name = 'python3'
  isolated = 0
  environment = 1
  user site = 1
  import site = 1
  sys._base_executable = '/usr/bin/python3'
  sys.base_prefix = '/usr'
  sys.base_exec_prefix = '/usr'
  sys.platlibdir = 'lib'
  sys.executable = '/usr/bin/python3'
  sys.prefix = '/usr'
  sys.exec_prefix = '/usr'
  sys.path = [
    '/usr/lib/python39.zip',
    '/usr/lib/python3.9',
    '/usr/lib/python3.9/lib-dynload',
  ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
ValueError: source code string cannot contain null bytes

Current thread 0x76f52980 (most recent call first):
<no Python frame>
dpkg: error processing package openmediavault (--configure):
 installed openmediavault package post-installation script subprocess returned error exit status 1
Errors were encountered while processing:
 openmediavault
Python path configuration:
  PYTHONHOME = (not set)
  PYTHONPATH = (not set)
  program name = 'python3'
  isolated = 0
  environment = 1
  user site = 1
  import site = 1
  sys._base_executable = '/usr/bin/python3'
  sys.base_prefix = '/usr'
  sys.base_exec_prefix = '/usr'
  sys.platlibdir = 'lib'
  sys.executable = '/usr/bin/python3'
  sys.prefix = '/usr'
  sys.exec_prefix = '/usr'
  sys.path = [
    '/usr/lib/python39.zip',
    '/usr/lib/python3.9',
    '/usr/lib/python3.9/lib-dynload',
  ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
ValueError: source code string cannot contain null bytes

Current thread 0x76fe3980 (most recent call first):
<no Python frame>
E: Sub-process /usr/bin/dpkg returned an error code (1)
pi@omv:~ $

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Soma · 11. Mai 2023

Zitat von PiUser

it is more or less the same error:

Never saw this before.

Did you changed any configuration on the system?

What is the output of:

dpkg -l | grep python

Should show:

Code

pi@panela:~ $ dpkg -l | grep python
ii  libpython3-stdlib:arm64              3.9.2-3                          arm64        interactive high-level object-oriented language (default python3 version)
ii  libpython3.9:arm64                   3.9.2-1                          arm64        Shared Python runtime library (version 3.9)
ii  libpython3.9-minimal:arm64           3.9.2-1                          arm64        Minimal subset of the Python language (version 3.9)
ii  libpython3.9-stdlib:arm64            3.9.2-1                          arm64        Interactive high-level object-oriented language (standard library, version 3.9)
ii  python-apt-common                    2.2.1                            all          Python interface to libapt-pkg (locales)
ii  python-is-python3                    3.9.2-1                          all          symlinks /usr/bin/python to python3
ii  python3                              3.9.2-3                          arm64        interactive high-level object-oriented language (default python3 version)
ii  python3-apt                          2.2.1                            arm64        Python 3 interface to libapt-pkg
ii  python3-cached-property              1.5.2-1                          all          Provides cached-property for decorating methods in classes (Python 3)
ii  python3-certifi                      2020.6.20-1                      all          root certificates for validating SSL certs and verifying TLS hosts (python3)
ii  python3-chardet                      4.0.0-1                          all          universal character encoding detector for Python3
ii  python3-click                        7.1.2-1                          all          Wrapper around optparse for command line utilities - Python 3.x
ii  python3-colorama                     0.4.4-1                          all          Cross-platform colored terminal text in Python - Python 3.x
ii  python3-colorzero                    1.1                              all          Construct, convert, and manipulate colors in a Pythonic manner.
ii  python3-dateutil                     2.8.1-6                          all          powerful extensions to the standard Python 3 datetime module
ii  python3-dbus                         1.2.16-5                         arm64        simple interprocess messaging system (Python 3 interface)
ii  python3-debconf                      1.5.77                           all          interact with debconf from Python 3
ii  python3-dialog                       3.5.1-1                          all          Python module for making simple terminal-based user interfaces
ii  python3-distro                       1.5.0-1                          all          Linux OS platform information API
ii  python3-distutils                    3.9.2-1                          all          distutils package for Python 3.x
ii  python3-dnspython                    2.0.0-1                          all          DNS toolkit for Python 3
ii  python3-docker                       4.1.0-1.2                        all          Python 3 wrapper to access docker.io's control socket
ii  python3-gpiozero                     1.6.2-1                          all          Simple API for controlling devices attached to a Pi's GPIO pins.
ii  python3-idna                         2.10-1                           all          Python IDNA2008 (RFC 5891) handling (Python 3)
ii  python3-jinja2                       2.11.3-1                         all          small but fast and easy to use stand-alone template engine
ii  python3-ldb                          2:2.2.3-2~deb11u2                arm64        Python 3 bindings for LDB
ii  python3-lib2to3                      3.9.2-1                          all          Interactive high-level object-oriented language (lib2to3)
ii  python3-lxml:arm64                   4.6.3+dfsg-0.1+deb11u1           arm64        pythonic binding for the libxml2 and libxslt libraries
ii  python3-markupsafe                   1.1.1-1+b3                       arm64        HTML/XHTML/XML string library for Python 3
ii  python3-minimal                      3.9.2-3                          arm64        minimal subset of the Python language (default python3 version)
ii  python3-msgpack                      1.0.0-6+b1                       arm64        Python 3 implementation of MessagePack format
ii  python3-natsort                      7.1.0-1                          all          Natural sorting for Python (Python3)
ii  python3-netifaces                    0.10.9-0.2+b3                    arm64        portable network interface information - Python 3.x
ii  python3-pkg-resources                52.0.0-4                         all          Package Discovery and Resource Access using pkg_resources
ii  python3-polib                        1.1.0-7                          all          Python 3 library to parse and manage gettext catalogs
ii  python3-pretty-yaml                  20.4.0-1                         all          module to produce pretty and readable YAML-serialized data (Python 3)
ii  python3-psutil                       5.8.0-1                          arm64        module providing convenience functions for managing processes (Python3)
ii  python3-pycryptodome                 3.9.7+dfsg1-1+b2                 arm64        cryptographic Python library (Python 3)
ii  python3-pyudev                       0.22.0-2                         all          Python3 bindings for libudev
ii  python3-requests                     2.25.1+dfsg-2                    all          elegant and simple HTTP library for Python3, built for human beings
ii  python3-rpi.gpio                     0.7.0-0.2+b2                     arm64        Module to control Raspberry Pi GPIO channels (Python 3)
ii  python3-samba                        2:4.13.13+dfsg-1~deb11u5         arm64        Python 3 bindings for Samba
ii  python3-six                          1.16.0-2                         all          Python 2 and 3 compatibility library (Python 3 interface)
ii  python3-spidev                       20200602~200721-1                arm64        Bindings for Linux SPI access through spidev (Python 3)
ii  python3-systemd                      234-3+b4                         arm64        Python 3 bindings for systemd
ii  python3-talloc:arm64                 2.3.1-2+b1                       arm64        hierarchical pool based memory allocator - Python3 bindings
ii  python3-tdb                          1.4.3-1+b1                       arm64        Python3 bindings for TDB
ii  python3-unidecode                    1.2.0-1                          all          ASCII transliterations of Unicode text (Python 3 module)
ii  python3-urllib3                      1.26.5-1~exp1                    all          HTTP library with thread-safe connection pooling for Python3
ii  python3-websocket                    0.57.0-1                         all          WebSocket client library - Python 3.x
ii  python3-yaml                         5.3.1-5                          arm64        YAML parser and emitter for Python3
ii  python3-zmq                          20.0.0-1+b1                      arm64        Python3 bindings for 0MQ library
ii  python3.9                            3.9.2-1                          arm64        Interactive high-level object-oriented language (version 3.9)
ii  python3.9-minimal                    3.9.2-1                          arm64        Minimal subset of the Python language (version 3.9)

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PiUser · 11. Mai 2023

No, I changed nothing, the last update worked.

Zitat

What is the output of:

dpkg -l | grep python

Code

pi@omv:~ $ dpkg -l | grep python
ii  libpython3-stdlib:armhf              3.9.2-3                          armhf        interactive high-level object-oriented language (default python3 version)
ii  libpython3.9:armhf                   3.9.2-1+rpi1                     armhf        Shared Python runtime library (version 3.9)
ii  libpython3.9-minimal:armhf           3.9.2-1+rpi1                     armhf        Minimal subset of the Python language (version 3.9)
ii  libpython3.9-stdlib:armhf            3.9.2-1+rpi1                     armhf        Interactive high-level object-oriented language (standard library, version 3.9)
ii  python-apt-common                    2.2.1                            all          Python interface to libapt-pkg (locales)
ii  python-is-python3                    3.9.2-1                          all          symlinks /usr/bin/python to python3
ii  python3                              3.9.2-3                          armhf        interactive high-level object-oriented language (default python3 version)
ii  python3-apt                          2.2.1                            armhf        Python 3 interface to libapt-pkg
ii  python3-cached-property              1.5.2-1                          all          Provides cached-property for decorating methods in classes (Python 3)
ii  python3-certifi                      2020.6.20-1                      all          root certificates for validating SSL certs and verifying TLS hosts (python3)
ii  python3-chardet                      4.0.0-1                          all          universal character encoding detector for Python3
ii  python3-click                        7.1.2-1                          all          Wrapper around optparse for command line utilities - Python 3.x
ii  python3-colorama                     0.4.4-1                          all          Cross-platform colored terminal text in Python - Python 3.x
ii  python3-colorzero                    1.1                              all          Construct, convert, and manipulate colors in a Pythonic manner.
ii  python3-dateutil                     2.8.1-6                          all          powerful extensions to the standard Python 3 datetime module
ii  python3-dbus                         1.2.16-5                         armhf        simple interprocess messaging system (Python 3 interface)
ii  python3-debconf                      1.5.77                           all          interact with debconf from Python 3
ii  python3-dialog                       3.5.1-1                          all          Python module for making simple terminal-based user interfaces
ii  python3-distro                       1.5.0-1                          all          Linux OS platform information API
ii  python3-dnspython                    2.0.0-1                          all          DNS toolkit for Python 3
ii  python3-gpiozero                     1.6.2-1                          all          Simple API for controlling devices attached to a Pi's GPIO pins.
ii  python3-idna                         2.10-1                           all          Python IDNA2008 (RFC 5891) handling (Python 3)
ii  python3-jinja2                       2.11.3-1                         all          small but fast and easy to use stand-alone template engine
ii  python3-kms++                        0~git20221104~171243+adc05b6-1   armhf        C++ library for kernel mode setting - python3 bindings
ii  python3-ldb                          2:2.2.3-2~deb11u2                armhf        Python 3 bindings for LDB
ii  python3-libcamera                    0~git20230302+923f5d70-1         armhf        complex camera support library (Python 3 bindings)
ii  python3-lxml:armhf                   4.6.3+dfsg-0.1+deb11u1           armhf        pythonic binding for the libxml2 and libxslt libraries
ii  python3-markupsafe                   1.1.1-1+b1                       armhf        HTML/XHTML/XML string library for Python 3
ii  python3-minimal                      3.9.2-3                          armhf        minimal subset of the Python language (default python3 version)
ii  python3-msgpack                      1.0.0-6                          armhf        Python 3 implementation of MessagePack format
ii  python3-natsort                      7.1.0-1                          all          Natural sorting for Python (Python3)
ii  python3-netifaces                    0.10.9-0.2+b1                    armhf        portable network interface information - Python 3.x
ii  python3-numpy                        1:1.19.5-1                       armhf        Fast array facility to the Python 3 language
ii  python3-picamera2                    0.3.9-1                          all          Libcamera based python library
ii  python3-pidng                        4.0.9-1                          armhf        Create Adobe DNG RAW files using Python (Python 3)
ii  python3-piexif                       1.1.3-1                          all          Exif manipulation with pure python script (Python 3)
ii  python3-pil:armhf                    8.1.2+dfsg-0.3+deb11u1           armhf        Python Imaging Library (Python3)
ii  python3-pkg-resources                52.0.0-4                         all          Package Discovery and Resource Access using pkg_resources
ii  python3-polib                        1.1.0-7                          all          Python 3 library to parse and manage gettext catalogs
ii  python3-prctl                        1.7-2+b2                         armhf        Python interface to the prctl() syscall (Python 3)
ii  python3-psutil                       5.8.0-1                          armhf        module providing convenience functions for managing processes (Python3)
ii  python3-pycryptodome                 3.9.7+dfsg1-1+b1                 armhf        cryptographic Python library (Python 3)
ii  python3-pyudev                       0.22.0-2                         all          Python3 bindings for libudev
ii  python3-requests                     2.25.1+dfsg-2                    all          elegant and simple HTTP library for Python3, built for human beings
ii  python3-rpi.gpio                     0.7.0-0.2+b1                     armhf        Module to control Raspberry Pi GPIO channels (Python 3)
ii  python3-samba                        2:4.13.13+dfsg-1~deb11u5         armhf        Python 3 bindings for Samba
ii  python3-simplejpeg                   1.6.4-1                          armhf        Simple package for fast JPEG encoding and decoding
ii  python3-six                          1.16.0-2                         all          Python 2 and 3 compatibility library (Python 3 interface)
ii  python3-spidev                       20200602~200721-1                armhf        Bindings for Linux SPI access through spidev (Python 3)
ii  python3-systemd                      234-3+b2                         armhf        Python 3 bindings for systemd
ii  python3-talloc:armhf                 2.3.1-2+b1                       armhf        hierarchical pool based memory allocator - Python3 bindings
ii  python3-tdb                          1.4.3-1+b1                       armhf        Python3 bindings for TDB
ii  python3-toml                         0.10.1-1                         all          library for Tom's Obvious, Minimal Language - Python 3.x
ii  python3-urllib3                      1.26.5-1~exp1                    all          HTTP library with thread-safe connection pooling for Python3
ii  python3-v4l2                         0.3.2-1                          all          Python bindings for the v4l2 userspace api
ii  python3-yaml                         5.3.1-5                          armhf        YAML parser and emitter for Python3
ii  python3-zmq                          20.0.0-1                         armhf        Python3 bindings for 0MQ library
ii  python3.9                            3.9.2-1+rpi1                     armhf        Interactive high-level object-oriented language (version 3.9)
ii  python3.9-minimal                    3.9.2-1+rpi1                     armhf        Minimal subset of the Python language (version 3.9)
pi@omv:~ $

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When I just enter "python3" in the ssh console the same error occurs, so I assume it has something to do with the Python configuration, but this is just a guess.

Soma · 11. Mai 2023

Zitat von PiUser

When I just enter "python3" in the ssh console the same error occurs, so I assume it has something to do with the Python configuration, but this is just a guess.

Since you have more packages than I recognize, you probably have installed other things outside a "vanilla OMV".

This is out of my knowledge.

Only thing I can occur is maybe your SDcard is corrupted or your python3 install.

Without any warranties, you can try to make a clone of the OS first (for failsafe) and then try to run the install script to see if it clears the errors.

Check that OMV is proper installed with dpkg -l | grep openm

If all says ii, run the script and let it finish:

OpenMediaVault-Plugin-Developers/installScript: script that installs omv-extras and openmediavault if not installed already. (github.com)

As for the python3 command, it should show:

Code

pi@panela:~ $ python3
Python 3.9.2 (default, Feb 28 2021, 17:03:44)
[GCC 10.2.1 20210110] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()
Use exit() or Ctrl-D (i.e. EOF) to exit
>>> exit()

PiUser · 11. Mai 2023

I only installled a few plugins but that was far before the last update.

Zitat von Soma

Check that OMV is proper installed with dpkg -l | grep openm

Code

pi@omv:~ $ dpkg -l | grep openm
iF  openmediavault                       6.3.10-2                         all          openmediavault - The open network attached storage solution
ii  openmediavault-cputemp               6.1.3                            all          cpu temperature plugin for openmediavault
ii  openmediavault-diskstats             6.0.3-1                          all          openmediavault disk monitoring plugin
ii  openmediavault-filebrowser           6.0.4-1                          all          openmediavault File Browser plugin
ii  openmediavault-flashmemory           6.2                              all          folder2ram plugin for openmediavault
ii  openmediavault-keyring               1.0                              all          GnuPG archive keys of the OpenMediaVault archive
ii  openmediavault-omvextrasorg          6.1.1                            all          OMV-Extras.org Package Repositories for OpenMediaVault
pi@omv:~ $

I think the first "iF" is because the 6.3.10-2 update is not properly configured.

Will try the script later.

Anyway thanks a lot for your help!

Soma · 11. Mai 2023

Zitat von PiUser

I think the first "iF" is because the 6.3.10-2 update is not properly configured.

Yes, dpkg CAPITAL letters means errors/issues:

command line - What do the various dpkg flags like 'ii' 'rc' mean? - Ask Ubuntu

More specific, the -F

I have to reiterate, make a clone of the OS prior to any attempt.

You will have a failsafe IMG of the SDcard (or USB stick) to come back to.

Sorry, can't help you more than this.

Problem while updating

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